*** empty log message ***

Cantera/clib/src/ctmultiphase.cpp

@@ -67,6 +67,10 @@ static bool checkPhase(int i, int n) {
     }
 }
 
+namespace Cantera {
+    int _equilflag(const char* xy);
+}
+
 extern "C" {  
 
     int DLL_EXPORT mix_new() {
@@ -180,7 +184,7 @@ extern "C" {
     doublereal DLL_EXPORT mix_equilibrate(int i, char* XY, 
         doublereal err, int maxiter) { 
         try {
-            return equilibrate(*_mix(i), XY, err, maxiter);
+            return equilibrate(*_mix(i), _equilflag(XY), err, maxiter);
         }
         catch (CanteraError) {
             return DERR;

Cantera/python/Cantera/mixture.py

@@ -61,13 +61,13 @@ class Mixture:
         """Delete the Mixture instance. The phase objects are not deleted."""
         _cantera.mix_del(self.__mixid)
 
-##     def __repr__(self):
+    def __str__(self):
-##         s = ''
+        s = ''
-##         for p in range(len(self._phases)):
+        for p in range(len(self._phases)):
-##             s += '\n*******************    Phase '+self._phases[p].name()+'    ******************************\n'
+            s += '\n*******************    Phase '+self._phases[p].name()+'    ******************************\n'
-##             s += '\n Moles: '+`self.phaseMoles(p)`+'\n'
+            s += '\n Moles: '+`self.phaseMoles(p)`+'\n'
-##             s += self._phases[p].__repr__()+'\n\n'
+            s += self._phases[p].__repr__()+'\n\n'
-##         return s
+        return s
 
     def _addPhase(self, phase = None, moles = 0.0):
         """Add a phase to the mixture."""
@@ -75,6 +75,32 @@ class Mixture:
             self._spnames.append(phase.speciesName(k))            
         _cantera.mix_addPhase(self.__mixid, phase.thermo_hndl(), moles)
 
+    def nPhases(self):
+        """Total number of phases defined for the mixture."""
+        return len(self._phases)
+
+    def phaseName(self, n):
+        """Name of phase n."""
+        return self._phases[n].name()
+
+    def phaseNames(self):
+        """Names of all phases in the order added."""
+        np = self.nPhases()
+        nm = []
+        for n in range(np):
+            nm.append(self.phaseName(n))
+        return nm
+
+    def phaseIndex(self, phase):
+        """Index of phase with name 'phase'"""
+        np = self.nPhases()
+        if type(phase) <> types.StringType:
+            return phase
+        for n in range(np):
+            if self.phaseName(n) == phase:
+                return n
+        return -1
+    
     def nElements(self):
         """Total number of elements present in the mixture."""
         return _cantera.mix_nElements(self.__mixid)
@@ -141,9 +167,16 @@ class Mixture:
     def pressure(self):
         """The pressure [Pa]."""
         return _cantera.mix_pressure(self.__mixid)    
-    def phaseMoles(self, n):
+    def phaseMoles(self, n = -1):
         """Moles of phase n."""
-        return _cantera.mix_phaseMoles(self.__mixid, n)
+        if n == -1:
+            np = self.nPhases()
+            moles = zeros(np,'d')
+            for m in range(np):
+                moles[m] = _cantera.mix_phaseMoles(self.__mixid, m)
+            return moles
+        else:   
+            return _cantera.mix_phaseMoles(self.__mixid, n)
     def setPhaseMoles(self, n, moles):
         """Set the number of moles of phase n."""
         _cantera.mix_setPhaseMoles(self.__mixid, n, moles)

Cantera/python/ctml_writer.py

@@ -1199,6 +1199,8 @@ class stoichiometric_solid(phase):
         self._tr = transport
 
     def conc_dim(self):
+        """A stoichiometric solid always has unit activity, so the
+        generalized concentration is 1 (dimensionless)."""
         return (0,0)
         
     def build(self, p):
@@ -1225,36 +1227,31 @@ class stoichiometric_liquid(stoichiometric_solid):
                  initial_state = None,
                  options = []):
         
-        stoichiometric_solid.__init__(self, name, 3, elements,
+        stoichiometric_solid.__init__(self, name, elements,
-                                      species, 'none',
+                                      species, density, transport,
                                       initial_state, options)
-        self._dens = density
-        self._pure = 1
-        if self._dens < 0.0:
-            raise CTI_Error('density must be specified.')
-        self._tr = transport
         
-class pure_solid(stoichiometric_solid):
+## class pure_solid(stoichiometric_solid):
-    """Deprecated. Use stoichiometric_solid"""
+##     """Deprecated. Use stoichiometric_solid"""
-    def __init__(self,
+##     def __init__(self,
-                 name = '',
+##                  name = '',
-                 elements = '',
+##                  elements = '',
-                 species = '',
+##                  species = '',
-                 density = -1.0,
+##                  density = -1.0,
-                 transport = 'None',
+##                  transport = 'None',
-                 initial_state = None,
+##                  initial_state = None,
-                 options = []):
+##                  options = []):
         
-        stoichiometric_solid.__init__(self, name, 3, elements,
+##         stoichiometric_solid.__init__(self, name, 3, elements,
-                                      species, 'none',
+##                                       species, 'none',
-                                      initial_state, options)
+##                                       initial_state, options)
-        self._dens = density
+##         self._dens = density
-        self._pure = 1
+##         self._pure = 1
-        if self._dens < 0.0:
+##         if self._dens < 0.0:
-            raise CTI_Error('density must be specified.')
+##             raise CTI_Error('density must be specified.')
-        self._tr = transport
+##         self._tr = transport
-        print 'WARNING: entry type pure_solid is deprecated.'
+##         print 'WARNING: entry type pure_solid is deprecated.'
-        print 'Use stoichiometric_solid instead.'
+##         print 'Use stoichiometric_solid instead.'
 
 
 class metal(phase):
@@ -1495,7 +1492,10 @@ if __name__ == "__main__":
 # $Revision$
 # $Date$
 # $Log$
-# Revision 1.8  2004-12-02 22:11:28  dggoodwin
+# Revision 1.9  2005-01-08 22:28:01  dggoodwin
+# *** empty log message ***
+#
+# Revision 1.8  2004/12/02 22:11:28  dggoodwin
 # *** empty log message ***
 #
 # Revision 1.7  2004/11/15 02:33:21  dggoodwin

Cantera/src/ChemEquil.h

@@ -174,9 +174,7 @@ namespace Cantera {
      * calculation.
      */
     inline void equilibrate(thermo_t& s, const char* XY) {
-        ChemEquil e;
+        equilibrate(s,_equilflag(XY));
-        e.equilibrate(s,_equilflag(XY));
-        s.setElementPotentials(e.elementPotentials());
     }
 
 }

Cantera/src/MultiPhase.cpp

@@ -1,4 +1,5 @@
 #include "MultiPhase.h"
+#include "MultiPhaseEquil.h"
 
 #include "ThermoPhase.h"
 #include "DenseMatrix.h"
@@ -19,6 +20,7 @@ namespace Cantera {
 
         // store its number of moles
         m_moles.push_back(moles);
+        m_temp_OK.push_back(true);
 
         // update the number of phases and the total number of
         // species
@@ -143,6 +145,22 @@ namespace Cantera {
         }
     }
 
+    /// Chemical potentials. Write into array \c mu the chemical
+    /// potentials of all species [J/kmol].
+    void MultiPhase::getValidChemPotentials(doublereal not_mu,
+        doublereal* mu) {
+        index_t i, loc = 0;
+        updatePhases();            
+        for (i = 0; i < m_np; i++) {
+            if (tempOK(i) || m_phase[i]->nSpecies() > 1) 
+                m_phase[i]->getChemPotentials(mu + loc);
+            else
+                fill(mu + loc, mu + loc + m_phase[i]->nSpecies(), not_mu);
+            loc += m_phase[i]->nSpecies();
+        }
+    }
+
+
     /// Chemical potentials. Write into array \c mu the chemical
     /// potentials of all species [J/kmol].
     void MultiPhase::getStandardChemPotentials(doublereal* mu) {
@@ -240,7 +258,23 @@ namespace Cantera {
             doublereal* x = m_moleFractions.begin() + loc;
             loc += nsp;
             m_phase[p]->setState_TPX(m_temp, m_press, x);
+            m_temp_OK[p] = true;
+            if (m_temp < m_phase[p]->minTemp() 
+                || m_temp > m_phase[p]->maxTemp()) m_temp_OK[p] = false;
         }
     }            
+
+    doublereal MultiPhase::equilibrate(int XY, doublereal err, 
+        int maxsteps) {
+        cout << "in equil" << endl;
+        init();
+        if (m_equil == 0) {
+            m_equil = new MultiPhaseEquil(this);
+        }
+        m_equil->equilibrate(XY, err, maxsteps);
+        delete m_equil;
+        m_equil = 0;
+    }
+
 }
 

Cantera/src/MultiPhase.h

@@ -7,6 +7,8 @@
 
 namespace Cantera {
 
+    class MultiPhaseEquil;
+
     /// A class for multiphase mixtures. The mixture can contain any
     /// number of phases of any type.  All phases have the same
     /// temperature and pressure, and a specified number of moles.
@@ -27,7 +29,7 @@ namespace Cantera {
         /// Constructor. The constructor takes no arguments, since
         /// phases are added using method addPhase.
         MultiPhase() : m_temp(0.0), m_press(0.0), 
-                       m_nel(0), m_nsp(0), m_init(false) {}
+                       m_nel(0), m_nsp(0), m_init(false), m_equil(0) {}
 
         /// Destructor. Does nothing. Class MultiPhase does not take 
         /// "ownership" (i.e. responsibility for destroying) the
@@ -93,6 +95,8 @@ namespace Cantera {
         /// potentials of all species [J/kmol].
         void getChemPotentials(doublereal* mu);
 
+        void getValidChemPotentials(doublereal not_mu, doublereal* mu);
+
         /// Chemical potentials. Write into array \c mu the chemical
         /// potentials of all species [J/kmol].
         void getStandardChemPotentials(doublereal* mu);
@@ -102,6 +106,10 @@ namespace Cantera {
             return m_temp;
         }
 
+        doublereal equilibrate(int XY, doublereal err = 1.0e-9, 
+            int maxsteps = 1000);
+
+
         /// Set the temperature [K].
         void setTemperature(doublereal T) {
             m_temp = T;
@@ -143,6 +151,10 @@ namespace Cantera {
 
         void setMoles(doublereal* n);
 
+        bool tempOK(index_t p) {
+            return m_temp_OK[p];
+        }
+
     protected:
 
         /// Set the states of the phase objects to the locally-stored
@@ -165,6 +177,8 @@ namespace Cantera {
         index_t m_nel; 
         index_t m_nsp;
         bool m_init;
+        vector<bool> m_temp_OK;
+        MultiPhaseEquil* m_equil;
     };
 
     inline std::ostream& operator<<(std::ostream& s, Cantera::MultiPhase& x) {

Cantera/src/MultiPhaseEquil.cpp

@@ -416,14 +416,6 @@ namespace Cantera {
 
     void MultiPhaseEquil::step(doublereal omega, vector_fp& deltaN) {
         index_t k, ik;
-        //if (m_iter > 500) {
-        //  for (ik = 0; ik < m_nsp; ik++) {
-                //k = m_order[ik];
-                //if (ik < m_nel) cout << "*";
-                //cout << m_mix->speciesName(m_species[k]) <<
-                //    ":    " << m_moles[k] << " += " << omega << " * " << deltaN[k] << endl;
-        //  }
-        //}
         if (omega < 0.0) 
             throw CanteraError("step","negative omega");
 
@@ -438,6 +430,7 @@ namespace Cantera {
             m_lastmoles[k] = m_moles[k];
             if (m_majorsp[k]) {
                 m_moles[k] += omega * deltaN[k];
+                if (m_moles[k] < 0.0) m_moles[k] = 0.0;
             }
             else {
                 m_moles[k] = fabs(m_moles[k])*fminn(10.0, exp(-m_deltaG_RT[ik - m_nel]));
@@ -544,7 +537,8 @@ namespace Cantera {
         // compute the gradient of G at this new position in the
         // current direction. If it is positive, then we have overshot
         // the minimum. In this case, interpolate back.
-        m_mix->getChemPotentials(m_mu.begin());
+        doublereal not_mu = 1.0e8;
+        m_mix->getValidChemPotentials(not_mu, m_mu.begin());
         doublereal grad1 = 0.0;
         for (k = 0; k < m_nsp; k++) {
             grad1 += m_work[k] * m_mu[m_species[k]];
@@ -573,8 +567,8 @@ namespace Cantera {
 
         dxi.resize(m_nsp - m_nel);
         computeN();
-
+        doublereal not_mu = 1.0e8;
-        m_mix->getChemPotentials(m_mu.begin());
+        m_mix->getValidChemPotentials(not_mu, m_mu.begin());
 
         for (j = 0; j < m_nsp - m_nel; j++) {
 
@@ -590,6 +584,7 @@ namespace Cantera {
 
             m_deltaG_RT[j] = dg_rt;
             fctr = 1.0;
+
             // if this is a formation reaction for a single-component phase, 
             // check whether reaction should be included
             ik = j + m_nel;

Cantera/src/SpeciesThermoFactory.cpp

@@ -195,8 +195,10 @@ namespace Cantera {
             getFloatArray(f0.child("floatArray"), c0, false);
             if (dualRange)
                 getFloatArray(f1ptr->child("floatArray"), c1, false);
-            else
+            else {
                 c1.resize(7,0.0);
+                copy(c0.begin(), c0.end(), c1.begin());
+            }
         }
         else if (fabs(tmax1 - tmin0) < 0.01) {
             tmin = tmin1;

Cantera/src/config.h

@@ -11,7 +11,7 @@
 // These flags turn on or off features that are still in
 // development and are not yet stable.
 
-#undef DEV_EQUIL
+#define DEV_EQUIL
 
 
 //------------------------ Fortran settings -------------------//
@@ -59,8 +59,8 @@ typedef  int          ftnlen;       // Fortran hidden string length type
 // The configure script defines this if the operatiing system is Mac
 // OS X, This used to add some Mac-specific directories to the default
 // data file search path.
-#define DARWIN 0
+#define DARWIN 1
-/* #undef HAS_SSTREAM */
+#define HAS_SSTREAM 1
 
 // Identify whether the operating system is cygwin's overlay of
 // windows, with gcc being used as the compiler.
@@ -68,19 +68,33 @@ typedef  int          ftnlen;       // Fortran hidden string length type
 
 // Identify whether the operating system is windows based, with
 // microsoft vc++ being used as the compiler
-#define WINMSVC
+/* #undef WINMSVC */
 
 //--------- Fonts for reaction path diagrams ----------------------
 #define RXNPATH_FONT "Helvetica"
 
 //--------------------- Python ------------------------------------
+// This path to the python executable is created during
+// Cantera's setup. It identifies the python executable
+// used to run Python to process .cti files. Note that this is only
+// used if environment variable PYTHON_CMD is not set.
+#define PYTHON_EXE "python"
+
 // If this is defined, the Cantera Python interface will use the
 // Numeric package; otherwise, it will use numarray.
-/* #define HAS_NUMERIC 1 */
+/* #undef HAS_NUMERIC */
+
+//--------------------- Cantera -----------------------------------
+
+/* #undef CANTERA_ROOT */
+// This data pathway is used to locate a directory where datafiles
+// are to be found. Note, the local directory is always searched
+// as well.
+#define CANTERA_DATA "/Applications/Cantera/data"
 
 #define INCL_PURE_FLUIDS 1
 
 //--------------------- compile options ----------------------------
-/* #define USE_PCH 1 */
+#define USE_PCH 1
 
 #endif

config.h

@@ -11,7 +11,7 @@
 // These flags turn on or off features that are still in
 // development and are not yet stable.
 
-#undef DEV_EQUIL
+#define DEV_EQUIL
 
 
 //------------------------ Fortran settings -------------------//
@@ -59,8 +59,8 @@ typedef  int          ftnlen;       // Fortran hidden string length type
 // The configure script defines this if the operatiing system is Mac
 // OS X, This used to add some Mac-specific directories to the default
 // data file search path.
-#define DARWIN 0
+#define DARWIN 1
-/* #undef HAS_SSTREAM */
+#define HAS_SSTREAM 1
 
 // Identify whether the operating system is cygwin's overlay of
 // windows, with gcc being used as the compiler.
@@ -68,19 +68,33 @@ typedef  int          ftnlen;       // Fortran hidden string length type
 
 // Identify whether the operating system is windows based, with
 // microsoft vc++ being used as the compiler
-#define WINMSVC
+/* #undef WINMSVC */
 
 //--------- Fonts for reaction path diagrams ----------------------
 #define RXNPATH_FONT "Helvetica"
 
 //--------------------- Python ------------------------------------
+// This path to the python executable is created during
+// Cantera's setup. It identifies the python executable
+// used to run Python to process .cti files. Note that this is only
+// used if environment variable PYTHON_CMD is not set.
+#define PYTHON_EXE "python"
+
 // If this is defined, the Cantera Python interface will use the
 // Numeric package; otherwise, it will use numarray.
-/* #define HAS_NUMERIC 1 */
+/* #undef HAS_NUMERIC */
+
+//--------------------- Cantera -----------------------------------
+
+/* #undef CANTERA_ROOT */
+// This data pathway is used to locate a directory where datafiles
+// are to be found. Note, the local directory is always searched
+// as well.
+#define CANTERA_DATA "/Applications/Cantera/data"
 
 #define INCL_PURE_FLUIDS 1
 
 //--------------------- compile options ----------------------------
-/* #define USE_PCH 1 */
+#define USE_PCH 1
 
 #endif

configure

@@ -108,7 +108,7 @@ PYTHON_CMD=${PYTHON_CMD:="default"}
 # The Cantera Python interface can be built with either the numarray
 # or Numeric packages. Set this to "y" to use Numeric, or anything
 # else to use numarray.
-USE_NUMERIC=${USE_NUMERIC:="y"}
+USE_NUMERIC=${USE_NUMERIC:="n"}
  
 # Set this to 'y' when site packages must be put in system directories
 # but Cantera tutorials must be put in user space.  An alternative to

tools/src/package4mac.in

@@ -12,6 +12,9 @@ RESDIR=$PKGDIR/Cantera/resources_dir
 NUMPYDIR=$PKGDIR/Numeric/root_dir/Library/Python/$PYVERSION
 NUMRESDIR=$PKGDIR/Numeric/resources_dir
 
+NUMARRAYPYDIR=$PKGDIR/numarray/root_dir/Library/Python/$PYVERSION
+NUMARRAYRESDIR=$PKGDIR/numarray/resources_dir
+
 # where Cantera has been installed
 instdir=/Applications/Cantera
 pylibdir=/Library/Python/$PYVERSION
@@ -24,11 +27,16 @@ $INSTALL -d $RESDIR
 $INSTALL -d $NUMPYDIR/Numeric
 $INSTALL -d $NUMRESDIR
 
+$INSTALL -d $NUMARRAYPYDIR/Numeric
+$INSTALL -d $NUMARRAYRESDIR
+
 rm -r -f $CTDIR/*
 rm -r -f $PYDIR/*
 rm -r -f $RESDIR/*
 rm -r -f $NUMPYDIR/*
 rm -r -f $NUMRESDIR/*
+rm -r -f $NUMARRAYPYDIR/*
+rm -r -f $NUMARRAYRESDIR/*
 
 cp -R -f $instdir/* $CTDIR
 chmod +x $CTDIR/bin/*
@@ -48,3 +56,5 @@ cp -f @ctroot@/License.rtf $RESDIR
 cp -R -f $pylibdir/Numeric/* $NUMPYDIR/Numeric
 cp -f $pylibdir/Numeric.pth $NUMPYDIR
 
+cp -R -f $pylibdir/numarray/* $NUMARRAYPYDIR/numarray
+